Polyploidy is a widespread phenomenon throughout eukaryotes, with important ecological and evolutionary consequences. Although genes operate as components of complex pathways and networks, polyploid changes in genes and gene expression have typically been evaluated as either individual genes or as a part of broad-scale analyses. Network analysis has been fruitful in associating genomic and other 'omic'-based changes with phenotype for many systems. In polyploid species, network analysis has the potential not only to facilitate a better understanding of the complex 'omic' underpinnings of phenotypic and ecological traits common to polyploidy, but also to provide novel insight into the interaction among duplicated genes and genomes. This adds perspective to the global patterns of expression (and other 'omic') change that accompany polyploidy and to the patterns of recruitment and/or loss of genes following polyploidization. While network analysis in polyploid species faces challenges common to other analyses of duplicated genomes, present technologies combined with thoughtful experimental design provide a powerful system to explore polyploid evolution. Here, we demonstrate the utility and potential of network analysis to questions pertaining to polyploidy with an example involving evolution of the transgressively superior cotton fibres found in polyploid Gossypium hirsutum. By combining network analysis with prior knowledge, we provide further insights into the role of profilins in fibre domestication and exemplify the potential for network analysis in polyploid species.
Ghirsutum_CRB252_5dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession CRB 252 fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-CRB252_5dpa_ATTCCT.fastq.gz
Ghirsutum_CRB252_10dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession CRB 252 fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-CRB252_10dpa_CAGATC.fastq.gz
Ghirsutum_CRB252_15dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession CRB 252 fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-CRB252_15dpa_GGCTAC.fastq.gz
Ghirsutum_CRB252_20dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession CRB 252 fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-CRB252_20dpa_ACAGTG.fastq.gz
Ghirsutum_Maxxa_5dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession Maxxa fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Maxxa_5dpa_ACTTGA.fastq.gz
Ghirsutum_Maxxa_10dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession Maxxa fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Maxxa_10dpa_CAGATC.fastq.gz
Ghirsutum_Maxxa_15dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession Maxxa fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Maxxa_15dpa_AGTTCC.fastq.gz
Ghirsutum_Maxxa_20dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession Maxxa fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Maxxa_20dpa_GTGAAA.fastq.gz
Ghirsutum_TM1_5dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TM-1 fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-TM1_5dpa_ACTGAT.fastq.gz
Ghirsutum_TM1_10dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TM-1 fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-TM1_10dpa_GTCCGC.fastq.gz
Ghirsutum_TM1_15dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TM-1 fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-TM1_15dpa_GTGGCC.fastq.gz
Ghirsutum_TM1_20dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TM-1 fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-TM1_20dpa_GTGAAA.fastq.gz
Ghirsutum_TX665_5dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX665 fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Tx665_5dpa_CTTGTA.fastq.gz
Ghirsutum_TX665_10dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX665 fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Tx665_10dpa_CGATGT.fastq.gz
Ghirsutum_TX665_15dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX665 fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Tx665_15dpa_TAGCTT.fastq.gz
Ghirsutum_TX665_20dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX665 fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Tx665_20dpa_GTTTCG.fastq.gz
Ghirsutum_TX2095_5dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX2095 fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Tx2095_5dpa_AGTCAA.fastq.gz
Ghirsutum_TX2095_10dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX2095 fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Tx2095_10dpa_TGACCA.fastq.gz
Ghirsutum_TX2095_15dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX2095 fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Tx2095_15dpa_GAGTGG.fastq.gz
Ghirsutum_TX2095_20dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum accession TX2095 fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Tx2095_20dpa_CGTACG.fastq.gz
Ghirsutum_yuc_5dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum var yucatanense fiber at 5 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Yuc_5dpa_TAGCTT.fastq.gz
Ghirsutum_yuc_10dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum var yucatanense fiber at 10 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Yuc_10_AGTTCC.fastq.gz
Ghirsutum_yuc_15dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum var yucatanense fiber at 15 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Yuc_15dpa_GATCAG.fastq.gz
Ghirsutum_yuc_20dpa
Illumina HiSeq 2500 100-bp single-end RNA-seq from Gossypium hirsutum var yucatanense fiber at 20 days post anthesis, grown in greenhouse; format: fastq.gz
Ghir-Yuc_20dpa_CCGTCC.fastq.gz